生物谷報道：主要用來釀酒的葡萄是一種古老的農(nóng)作物,，有證據(jù)顯示它在新石器時代和銅器時代早期就存在了,。雖然人們對種植培養(yǎng)過程如何影響收獲的葡萄的治療已經(jīng)有了較多的了解,，但是對葡萄本身的了解卻并不算充分。發(fā)表在本周PLoS ONE雜志上的一篇文章公布了高質(zhì)量的葡萄（Pinot Noir grape）的基因組序列草圖,。
這種葡萄的基因組分散在19隊染色體中,，并且其長度大約有5.046億個堿基對。由意大利科學(xué)家進(jìn)行的這項研究使用一種鳥槍測序方法對葡萄基因組進(jìn)行了測序,。與此同時,，葡萄葉綠體基因在也完成了測序。
葡萄是基因在相對較小的一種農(nóng)作物,，其大小與水稻和楊樹相似,，比小麥和玉米則要小的多。然而,，測序這個基因組則因為染色體對之間的雜合性程度高而變得很復(fù)雜,。事實上，與之前公布的兩個基因在存在很大的變異性,。
而且,，研究組在確定出的29585個基因中的87％的基因中發(fā)現(xiàn)了超過兩百萬個單核苷酸多肽性（SNP）——這使得測序過程變得非常困難。
這個研究組還能提供有關(guān)葡萄進(jìn)化的重要線索,。許多植物基因組都是由較小的祖先基因組經(jīng)過至少一次復(fù)制得來的,。葡萄是否也是這種情況還存在爭議,，但是這項新研究則清楚地證實19個染色體中的10個是由復(fù)制得來,。
研究人員稱，Pinot Noir基因組降能夠未培育能抗病且不會影響紅酒質(zhì)量的葡萄新品種提供了一個無價的工具,。
此前,，兩項公布在《BMC 基因組學(xué)》雜志上的兩篇新研究論文提供了一系列有關(guān)果實成熟的新遺傳信息，而果實的成熟對商業(yè)價值非常重要,。葡萄的基因表達(dá)分析揭示出兩個與葡萄的綠色階段和變紅階段相對應(yīng)的不同的分子和功能階段。研究人員公布了首個生物化學(xué)證據(jù)證實，在顏色過渡期發(fā)生著活性氧的累積,。
意大利IASMA研究中心的Stefania Pilati和同事分析了正在成熟的加州紅葡萄，以確定出果實成熟基因并研究季節(jié)對該過程的影響,。他們發(fā)現(xiàn),，超過1400個成熟特異性基因的表達(dá)在三個不同的生長季節(jié)中發(fā)生相似的波動,，其中一小類基因則受到氣候條件的強(qiáng)烈影響,。
在綠果階段，大量的與激素信號和轉(zhuǎn)錄調(diào)節(jié)有關(guān)的基因被調(diào)節(jié)——這意味著大規(guī)模的細(xì)胞代謝過程被重排,。生長素,、乙烯和光起到關(guān)鍵作用,。在之后的成熟期,，細(xì)胞壁組織和生物發(fā)生、糖類和次級代謝和壓力應(yīng)答相關(guān)基因則開始起作用,。此時，光合作用受到強(qiáng)烈抑制,。這些轉(zhuǎn)錄事件與果實軟化和糖,、顏色和香味化合物的積累過程相一致，而這些都決定著最終葡萄的品質(zhì),。在兩個階段的轉(zhuǎn)折點上,，研究人員發(fā)現(xiàn)一種與H2O2有關(guān)的氧化力和抗氧化酶網(wǎng)絡(luò)的一種廣泛的調(diào)整。
與此同時,，來自美國內(nèi)華達(dá)州大學(xué)和波士頓大學(xué)醫(yī)學(xué)院的Laurent G. Deluc和同事對V. vinifera Cavernet Sauvignon進(jìn)行了進(jìn)一步的研究,，他們分析了葡萄果實發(fā)育的7個不同的階段。該研究組確定出,，在一系列相關(guān)過程中起關(guān)鍵作用的基因的mRNA在整個發(fā)育過程中發(fā)生了顯著的變化,。相關(guān)過程包括有機(jī)和氨基酸代謝、光合作用,、碳循化和抗病性,。
原始出處:
PLoS ONE
Received: October 5, 2007; Accepted: November 21, 2007; Published: December 19, 2007
A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety
Riccardo Velasco1*#, Andrey Zharkikh2#, Michela Troggio1#, Dustin A. Cartwright1,2, Alessandro Cestaro1, Dmitry Pruss2, Massimo Pindo1, Lisa M. FitzGerald2, Silvia Vezzulli1, Julia Reid2, Giulia Malacarne1, Diana Iliev2, Giuseppina Coppola1, Bryan Wardell2, Diego Micheletti1, Teresita Macalma2, Marco Facci1, Jeff T. Mitchell2, Michele Perazzolli1, Glenn Eldredge2, Pamela Gatto1, Rozan Oyzerski2, Marco Moretto1, Natalia Gutin2, Marco Stefanini1, Yang Chen2, Cinzia Segala1, Christine Davenport2, Lorenzo Demattè1, Amy Mraz5, Juri Battilana1, Keith Stormo5, Fabrizio Costa1, Quanzhou Tao5, Azeddine Si-Ammour1, Tim Harkins4, Angie Lackey4, Clotilde Perbost3, Bruce Taillon3, Alessandra Stella6, Victor Solovyev9, Jeffrey A. Fawcett7, Lieven Sterck7, Klaas Vandepoele7, Stella M. Grando1, Stefano Toppo8, Claudio Moser1, Jerry Lanchbury2, Robert Bogden5, Mark Skolnick2, Vittorio Sgaramella6, Satish K. Bhatnagar2, Paolo Fontana1, Alexander Gutin2, Yves Van de Peer7, Francesco Salamini6, Roberto Viola1
1 IASMA Research Center, San Michele all'Adige, Trento, Italy, 2 Myriad Genetics Inc, Salt Lake City, Utah, United States of America, 3 454 Life Sciences Corporation, Branford, Connecticut, United States of America, 4 Roche Diagnostics Corporation, Roche Applied Science, Indianapolis, Indiana, United States of America, 5 Amplicon Express Inc., Pullman, Washington, United States of America, 6 Technology Park Lodi, Lodi, Italy, 7 Department of Plant Systems Biology, VIB, Gent University, Gent, Belgium, 8 Department of Biological Chemistry, Padova University, Padova, Italy, 9 Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom
Abstract
Background
Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented.
Principal Findings
We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before).
Conclusions
Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.
Table 1. Number and sizes of assembled sequences in Mb.
